Summary: Clp protease
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This is the Wikipedia entry entitled "CLP protease family". More...
CLP protease family Edit Wikipedia article
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Clp protease Provide feedback
The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. P48254 has lost all of these active site residues and is therefore inactive. P42379 contains two large insertions, P42380 contains one large insertion.
Literature references
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Wang J, Hartling JA, Flanagan JM; , Cell 1997;91:447-456.: The structure of ClpP at 2.3 angstroms resolution suggests a model for ATP-dependent proteolysis. PUBMED:9390554 EPMC:9390554
Internal database links
SCOOP: | ECH_1 Peptidase_S49 SDH_sah |
External database links
MEROPS: | S14 |
PROSITE: | PDOC00358 |
SCOP: | 1tyf |
This tab holds annotation information from the InterPro database.
InterPro entry IPR023562
This entry includes peptidases from the MEROPS peptidase family S14, including ClpP endopeptidase and translocation-enhancing protein TepA.
ClpP is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin [ PUBMED:2197275 ]. It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence of ATP [ PUBMED:2197275 ], although the P subunit alone does possess some catalytic activity. Proteases highly similar to ClpP have been found to be encoded in the genome of bacteria, metazoa, some viruses and in the chloroplast of plants. A number of the proteins in this family are classified as non-peptidase homologues as they have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity.
Translocation-enhancing protein TepA displays sequence similarity to ClpP. It is required for efficient translocation of pre-proteins across the membrane [ PUBMED:10455123 ].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan ClpP_crotonase (CL0127), which has the following description:
This family includes several peptidases of peptidase clan SK as well as crotonase like proteins.
The clan contains the following 10 members:
ACCA Carboxyl_trans CLP_protease ECH_1 ECH_2 MdcE Peptidase_S41 Peptidase_S49 Peptidase_S49_N SDH_sahAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (64) |
Full (20328) |
Representative proteomes | UniProt (89051) |
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RP15 (3197) |
RP35 (10480) |
RP55 (20029) |
RP75 (32206) |
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HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (64) |
Full (20328) |
Representative proteomes | UniProt (89051) |
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RP15 (3197) |
RP35 (10480) |
RP55 (20029) |
RP75 (32206) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Prosite |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 64 |
Number in full: | 20328 |
Average length of the domain: | 173.80 aa |
Average identity of full alignment: | 38 % |
Average coverage of the sequence by the domain: | 74.61 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 182 | ||||||||||||
Family (HMM) version: | 25 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CLP_protease domain has been found. There are 1262 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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